8BGL | pdb_00008bgl

Structure of the dimeric rsCherryRev1.4

• PDB DOI: https://doi.org/10.2210/pdb8BGL/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Discosoma sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-10-28 Released: 2023-02-15 
• Deposition Author(s): Bui, T.Y.H., Van Meervelt, L.
• Funding Organization(s): Other government, KU Leuven

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

An unusual disulfide-linked dimerization in the fluorescent protein rsCherryRev1.4.

Bui, T.Y.H., Dedecker, P., Van Meervelt, L.

(2023) Acta Crystallogr F Struct Biol Commun 79: 38-44

• PubMed: 36748340 
• DOI: https://doi.org/10.1107/S2053230X23000572
• Primary Citation Related Structures: 
  8BGL


• PubMed Abstract: 
  

  rsCherryRev1.4 has been reported as one of the reversibly photoswitchable variants of mCherry, and is an improved version with a faster off-switching speed and lower switching fatigue at high light intensities than its precursor rsCherryRev. However, rsCherryRev1.4 still has some limitations such as a tendency to dimerize as well as complex photophysical properties. Here, the crystal structure of rsCherryRev1.4 was determined at a resolution of 2 Å and it was discovered that it forms a dimer that shows disulfide bonding between the protomers. Mutagenesis, gel electrophoresis and size-exclusion chromatography strongly implicate Cys24 in this process. Replacing Cys24 in rsCherryRev1.4 resulted in a much lower tendency towards dimerization, while introducing Cys24 into mCherry correspondingly increased its dimerization. In principle, this finding opens the possibility of developing redox sensors based on controlled dimerization via disulfide cross-linking in fluorescent proteins, even though the actual application of engineering such sensors still requires additional research.

---

Organizational Affiliation: 
• Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.6 kDa 
• Atom Count: 3,792 
• Modeled Residue Count: 436 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PAmCherry1 protein	A, B	267	Discosoma sp.	Mutation(s): 2  Gene Names: PAmCherry, PAmCherry1
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8  Go to UniProtKB:  Q9U6Y8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	D [auth A], E [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA	A, B	L-PEPTIDE LINKING	C4 H9 N O2		ALA
Q2K	A, B	L-PEPTIDE LINKING	C9 H11 N3 O4 S		MET, TYR, GLY
QYX	A, B	L-PEPTIDE LINKING	C16 H18 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.104	α = 90
b = 48.822	β = 101.16
c = 99.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Bui, T.Y.H., Van Meervelt, L.

---

Funding Organization	Location	Grant Number
Other government		911 project
KU Leuven	Belgium	--

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-04-05
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-02-07
  Changes: Refinement description
• Version 3.0: 2024-07-24
  Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 3.1: 2024-10-16
  Changes: Structure summary